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Liu G, Pan Q, Dai Y, Wang X, Li M, Zhu P, Zhou X. Phylogenomics of Afrotherian mammals and improved resolution of extant Paenungulata. Mol Phylogenet Evol 2024; 195:108047. [PMID: 38460890 DOI: 10.1016/j.ympev.2024.108047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/19/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
Molecular investigations have gathered a diverse set of mammals-predominantly African natives like elephants, hyraxes, and aardvarks-into a clade known as Afrotheria. Nevertheless, the precise phylogenetic relationships among these species remain contentious. Here, we sourced orthologous markers and ultraconserved elements to discern the interordinal connections among Afrotherian mammals. Our phylogenetic analyses bolster the common origin of Afroinsectiphilia and Paenungulata, and propose Afrosoricida as the closer relative to Macroscelidea rather than Tubulidentata, while also challenging the notion of Sirenia and Hyracoidea as sister taxa. The approximately unbiased test and the gene concordance factor uniformly recognized the alliance of Proboscidea with Hyracoidea as the dominant topology within Paenungulata. Investigation into sites with extremly high phylogenetic signal unveiled their potential to intensify conflicts in the Paenungulata topology. Subsequent exploration suggested that incomplete lineage sorting was predominantly responsible for the observed contentious relationships, whereas introgression exerted a subsidiary influence. The divergence times estimated in our study hint at the Cretaceous-Paleogene (K-Pg) extinction event as a catalyst for Afrotherian diversification. Overall, our findings deliver a tentative but insightful overview of Afrotheria phylogeny and divergence, elucidating these relationships through the lens of phylogenomics.
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Affiliation(s)
- Gaoming Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Pan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yichen Dai
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meng Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Pingfen Zhu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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2
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Kuderna LFK, Gao H, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Rogers J, Farh KKH, Marques Bonet T. A global catalog of whole-genome diversity from 233 primate species. Science 2023; 380:906-913. [PMID: 37262161 DOI: 10.1126/science.abn7829] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/06/2023] [Indexed: 06/03/2023]
Abstract
The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.
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Affiliation(s)
- Lukas F K Kuderna
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Martin Kuhlwilm
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Austria
| | - Joseph D Orkin
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Département d'anthropologie, Université de Montréal, 3150 Jean-Brillant, Montréal, QC H3T 1N8, Canada
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Alejandro Valenzuela
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Estrada da Bexiga 2584, CEP 69553-225, Tefé, Amazonas, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Av. Franklin D. Roosevelt 50, CP 160/12, B-1050 Brussels Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
| | | | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City. UT 84102, USA
| | | | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
| | - João Valsecchi
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Amazonas, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia - RedeFauna, Manaus, Amazonas, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica - ComFauna, Iquitos, Loreto, Peru
| | - Malu Messias
- Universidade Federal de Rondônia, Porto Velho, Rondônia, Brazil
| | | | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Rogerio Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, MT, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
- Department of Biology, Trinity University, San Antonio, TX 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Jane Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | | | - Sree Kanthaswamy
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ 85004, USA
| | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, Addis Ababa, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Long Zhou
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Shangcheng District, Hangzhou 310006, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office, P.O. Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
| | - Esther Lizano
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Arcadi Navarro
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Av. Doctor Aiguader, N88, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C. Wellington 30, 08005 Barcelona, Spain
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Jessica Lee
- Mandai Nature, 80 Mandai Lake Road, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK, and School of Geosciences, Drummond Street, Edinburgh EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
- Department of Medical Genetics, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Tomas Marques Bonet
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010 Barcelona, Spain
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3
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Li Y, Brinkworth A, Green E, Oyston J, Wills M, Ruta M. Divergent vertebral formulae shape the evolution of axial complexity in mammals. Nat Ecol Evol 2023; 7:367-381. [PMID: 36878987 PMCID: PMC9998275 DOI: 10.1038/s41559-023-01982-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 01/03/2023] [Indexed: 03/08/2023]
Abstract
Complexity, defined as the number of parts and their degree of differentiation, is a poorly explored aspect of macroevolutionary dynamics. The maximum anatomical complexity of organisms has undoubtedly increased through evolutionary time. However, it is unclear whether this increase is a purely diffusive process or whether it is at least partly driven, occurring in parallel in most or many lineages and with increases in the minima as well as the means. Highly differentiated and serially repeated structures, such as vertebrae, are useful systems with which to investigate these patterns. We focus on the serial differentiation of the vertebral column in 1,136 extant mammal species, using two indices that quantify complexity as the numerical richness and proportional distribution of vertebrae across presacral regions and a third expressing the ratio between thoracic and lumbar vertebrae. We address three questions. First, we ask whether the distribution of complexity values in major mammal groups is similar or whether clades have specific signatures associated with their ecology. Second, we ask whether changes in complexity throughout the phylogeny are biased towards increases and whether there is evidence of driven trends. Third, we ask whether evolutionary shifts in complexity depart from a uniform Brownian motion model. Vertebral counts, but not complexity indices, differ significantly between major groups and exhibit greater within-group variation than recognized hitherto. We find strong evidence of a trend towards increasing complexity, where higher values propagate further increases in descendant lineages. Several increases are inferred to have coincided with major ecological or environmental shifts. We find support for multiple-rate models of evolution for all complexity metrics, suggesting that increases in complexity occurred in stepwise shifts, with evidence for widespread episodes of recent rapid divergence. Different subclades evolve more complex vertebral columns in different configurations and probably under different selective pressures and constraints, with widespread convergence on the same formulae. Further work should therefore focus on the ecological relevance of differences in complexity and a more detailed understanding of historical patterns.
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Affiliation(s)
- Yimeng Li
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK.,Nanjing Institute of Geology and Palaeontology, CAS, Nanjing, China
| | - Andrew Brinkworth
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Emily Green
- Joseph Banks Laboratories, Department of Life Sciences, University of Lincoln, Lincoln, UK
| | - Jack Oyston
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Matthew Wills
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK.
| | - Marcello Ruta
- Joseph Banks Laboratories, Department of Life Sciences, University of Lincoln, Lincoln, UK.
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4
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Molecular phylogenies map to biogeography better than morphological ones. Commun Biol 2022; 5:521. [PMID: 35641555 PMCID: PMC9156683 DOI: 10.1038/s42003-022-03482-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic relationships are inferred principally from two classes of data: morphological and molecular. Currently, most phylogenies of extant taxa are inferred from molecules and when morphological and molecular trees conflict the latter are often preferred. Although supported by simulations, the superiority of molecular trees has rarely been assessed empirically. Here we test phylogenetic accuracy using two independent data sources: biogeographic distributions and fossil first occurrences. For 48 pairs of morphological and molecular trees we show that, on average, molecular trees provide a better fit to biogeographic data than their morphological counterparts and that biogeographic congruence increases over research time. We find no significant differences in stratigraphic congruence between morphological and molecular trees. These results have implications for understanding the distribution of homoplasy in morphological data sets, the utility of morphology as a test of molecular hypotheses and the implications of analysing fossil groups for which molecular data are unavailable. Using biogeographical and phylogenetic data, it is shown that molecular trees fit species geographical data better than trees inferred from morphology, and that these differences are not simply due to better tree resolution.
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5
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Sarko DK, Reep RL. Parcellation in the dorsal column nuclei of Florida manatees (
Trichechus manatus latirostris
) and rock hyraxes (
Procavia capensis
) indicates the presence of body barrelettes. J Comp Neurol 2022; 530:2113-2131. [DOI: 10.1002/cne.25323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 03/10/2022] [Accepted: 03/15/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Diana K. Sarko
- Department of Anatomy Southern Illinois University School of Medicine Carbondale Illinois USA
| | - Roger L. Reep
- Department of Physiological Sciences University of Florida Gainesville Florida USA
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6
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Gavazzi LM, Kjosness KM, Reno PL. Ossification pattern of the unusual pisiform in two-toed (Choloepus) and three-toed sloths (Bradypus). Anat Rec (Hoboken) 2021; 305:1804-1819. [PMID: 34779120 DOI: 10.1002/ar.24832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/06/2022]
Abstract
Two-toed (Choloepus sp.) and three-toed (Bradypus sp.) sloths possess short, rounded pisiforms that are rare among mammals and differ from other members of Xenarthra like the giant anteater (Myrmecophaga tridactyla) which retain elongated, rod-like pisiforms in common with most mammals. Using photographs, radiographs, and μCT, we assessed ossification patterns in the pisiform and the paralogous tarsal, the calcaneus, for two-toed sloths, three-toed sloths, and giant anteaters to determine the process by which pisiform reduction occurs in sloths and compare it to other previously studied examples of pisiform reduction in humans and orangutans. Both extant sloth genera achieve pisiform reduction through the loss of a secondary ossification center and the likely disruption of the associated growth plate based on an unusually porous subchondral surface. This represents a third unique mechanism of pisiform reduction among mammals, along with primary ossification center loss in humans and retention of two ossification centers with likely reduced growth periods in orangutans. Given the remarkable similarities between two-toed and three-toed sloth pisiform ossification patterns and the presence of pisiform reduction in fossil sloths, extant sloth pisiform morphology does not appear to represent a recent convergent adaptation to suspensory locomotion, but instead is likely to be an ancestral trait of Folivora that emerged early in the radiation of extant and fossil sloths.
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Affiliation(s)
- Lia M Gavazzi
- School of Biomedical Sciences, Kent State University, Kent, Ohio, USA.,Musculoskeletal Research Group, Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio, USA
| | - Kelsey M Kjosness
- Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, Pennsylvania, USA
| | - Philip L Reno
- Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, Pennsylvania, USA
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7
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Hautier L, Tabuce R, Mourlam MJ, Kassegne KE, Amoudji YZ, Orliac M, Quillévéré F, Charruault AL, Johnson AKC, Guinot G. New Middle Eocene proboscidean from Togo illuminates the early evolution of the elephantiform-like dental pattern. Proc Biol Sci 2021; 288:20211439. [PMID: 34641726 PMCID: PMC8511763 DOI: 10.1098/rspb.2021.1439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/16/2021] [Indexed: 11/12/2022] Open
Abstract
Africa has played a pivotal role in the evolution of early proboscideans (elephants and their extinct relatives), yet vast temporal and geographical zones remain uncharted on the continent. A long hiatus encompassing most of the Eocene (Ypresian to the Early Priabonian, around 13 Myr timespan) considerably hampers our understanding of the early evolutionary history of the group. It is notably the case with the origin of its most successful members, the Elephantiformes, i.e. all elephant-like proboscideans most closely related to modern elephants. Here, we describe a proboscidean lower molar discovered in Lutetian phosphate deposits from Togo, and name a new genus and species, Dagbatitherium tassyi. We show that Dagbatitherium displays several elephantiform dental characteristics such as a three-layered Schmelzmuster, the presence of a mesoconid, transversely enlarged buccal cusps and the individualization of a third lophid closely appressed to a minute distal cingulid. Dagbatitherium represents a stem Elephantiformes, pushing back the origin of the group by about 10 Myr, i.e. a third of its currently known evolutionary history. More importantly, Dagbatitherium potentially unlocks the puzzle of the origin of the unique elephantiform tooth crown organization by bridging a critical temporal and morphological gap between early bunodont incipiently bilophodont proboscidean taxa and more derived elephantiforms.
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Affiliation(s)
- Lionel Hautier
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, CNRS, IRD, Cc 064, place Eugène Bataillon, Montpellier Cedex 5 34095, France
| | - Rodolphe Tabuce
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, CNRS, IRD, Cc 064, place Eugène Bataillon, Montpellier Cedex 5 34095, France
| | - Mickaël J. Mourlam
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, CNRS, IRD, Cc 064, place Eugène Bataillon, Montpellier Cedex 5 34095, France
| | | | - Yawovi Zikpi Amoudji
- Département de Géologie, Faculté des Sciences, Université de Lomé, Lomé B.P. 1515, Togo
| | - Maëva Orliac
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, CNRS, IRD, Cc 064, place Eugène Bataillon, Montpellier Cedex 5 34095, France
| | - Frédéric Quillévéré
- Univ Lyon, Université Claude Bernard Lyon 1, ENS de Lyon, CNRS, UMR 5276 LGL-TPE, Villeurbanne 69622, France
| | - Anne-Lise Charruault
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, CNRS, IRD, Cc 064, place Eugène Bataillon, Montpellier Cedex 5 34095, France
| | | | - Guillaume Guinot
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, CNRS, IRD, Cc 064, place Eugène Bataillon, Montpellier Cedex 5 34095, France
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8
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Hofmann R, Lehmann T, Warren DL, Ruf I. The squirrel is in the detail: Anatomy and morphometry of the tail in Sciuromorpha (Rodentia, Mammalia). J Morphol 2021; 282:1659-1682. [PMID: 34549832 DOI: 10.1002/jmor.21412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 09/09/2021] [Accepted: 09/15/2021] [Indexed: 11/07/2022]
Abstract
In mammals, the caudal vertebrae are certainly among the least studied elements of their skeleton. However, the tail plays an important role in locomotion (e.g., balance, prehensility) and behavior (e.g., signaling). Previous studies largely focused on prehensile tails in Primates and Carnivora, in which certain osteological features were selected and used to define tail regions (proximal, transitional, distal). Interestingly, the distribution pattern of these anatomical characters and the relative proportions of the tail regions were similar in both orders. In order to test if such tail regionalization can be applied to Rodentia, we investigated the caudal vertebrae of 20 Sciuridae and six Gliridae species. Furthermore, we examined relationships between tail anatomy/morphometry and locomotion. The position of selected characters along the tail was recorded and their distribution was compared statistically using Spearman rank correlation. Vertebral body length (VBL) was measured to calculate the proportions of each tail region and to perform procrustes analysis on the shape of relative vertebral body length (rVBL) progressions. Our results show that tail regionalization, as defined for Primates and Carnivora, can be applied to almost all investigated squirrels, regardless of their locomotor category. Moreover, major locomotor categories can be distinguished by rVBL progression and tail region proportions. In particular, the small flying squirrels Glaucomys volans and Hylopetes sagitta show an extremely short transitional region. Likewise, several semifossorial taxa can be distinguished by their short distal region. Moreover, among flying squirrels, Petaurista petaurista shows differences with the small flying squirrels, mirroring previous observations on locomotory adaptations based on their inner ear morphometry. Our results show furthermore that the tail region proportions of P. petaurista, phylogenetically more basal than the small flying squirrels, are similar to those of bauplan-conservative arboreal squirrels.
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Affiliation(s)
- Rebecca Hofmann
- Abteilung Messelforschung und Mammalogie, Senckenberg Forschungsinstitut und Naturmuseum Frankfurt, Frankfurt am Main, Germany.,Institut für Geowissenschaften, Goethe-Universität, Frankfurt am Main, Germany
| | - Thomas Lehmann
- Abteilung Messelforschung und Mammalogie, Senckenberg Forschungsinstitut und Naturmuseum Frankfurt, Frankfurt am Main, Germany
| | - Dan L Warren
- Senckenberg Biodiversität und Klima Forschungszentrum, Frankfurt am Main, Germany.,Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Irina Ruf
- Abteilung Messelforschung und Mammalogie, Senckenberg Forschungsinstitut und Naturmuseum Frankfurt, Frankfurt am Main, Germany.,Institut für Geowissenschaften, Goethe-Universität, Frankfurt am Main, Germany
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9
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Asher RJ, Smith MR. Phylogenetic Signal and Bias in Paleontology. Syst Biol 2021; 71:986-1008. [PMID: 34469583 PMCID: PMC9248965 DOI: 10.1093/sysbio/syab072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/24/2021] [Accepted: 08/27/2021] [Indexed: 11/12/2022] Open
Abstract
An unprecedented amount of evidence now illuminates the phylogeny of living mammals and birds on the Tree of Life. We use this tree to measure phylogenetic value of data typically used in paleontology (bones and teeth) from six datasets derived from five published studies. We ask three interrelated questions: 1) Can these data adequately reconstruct known parts of the Tree of Life? 2) Is accuracy generally similar for studies using morphology, or do some morphological datasets perform better than others? 3) Does the loss of non-fossilizable data cause taxa to occur in misleadingly basal positions? Adding morphology to DNA datasets usually increases congruence of resulting topologies to the well corroborated tree, but this varies among morphological datasets. Extant taxa with a high proportion of missing morphological characters can greatly reduce phylogenetic resolution when analyzed together with fossils. Attempts to ameliorate this by deleting extant taxa missing morphology are prone to decreased accuracy due to long-branch artefacts. We find no evidence that fossilization causes extinct taxa to incorrectly appear at or near topologically basal branches. Morphology comprises the evidence held in common by living taxa and fossils, and phylogenetic analysis of fossils greatly benefits from inclusion of molecular and morphological data sampled for living taxa, whatever methods are used for phylogeny estimation.
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Affiliation(s)
- Robert J Asher
- Department of Zoology, Downing St., University of Cambridge CB2 3EJ, UK
| | - Martin R Smith
- Department of Earth Sciences, Lower Mount Joy, Durham University, Durham DH1 3LE, UK
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10
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Abramov AV. An annotated checklist of the insectivores (Mammalia, Eulipotyphla) of Laos. Zootaxa 2021; 5006:13-25. [PMID: 34810591 DOI: 10.11646/zootaxa.5006.1.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Indexed: 11/04/2022]
Abstract
An annotated checklist of the insectivorous mammals (order Eulipotyphla) of Laos is presented for the first time. The checklist is based on an extensive literature review and an examination of available museum specimens from world collections. Confirmed fauna of eulipotyphlans includes 11 species from 7 genera and 3 families. Additionally, several species which are known from neighbouring countries and could potentially occur in Laos are included in this checklist. According to these data, the Laotian fauna can include at least 23 species in 11 genera.
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Affiliation(s)
- Alexei V Abramov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, Saint Petersburg 199034, Russia..
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11
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Wölfer J, Aschenbach T, Michel J, Nyakatura JA. Mechanics of Arboreal Locomotion in Swinhoe’s Striped Squirrels: A Potential Model for Early Euarchontoglires. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.636039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Differences between arboreal and terrestrial supports likely pose less contrasting functional demands on the locomotor system at a small body size. For arboreal mammals of small body size, asymmetrical gaits have been demonstrated to be advantageous to increase dynamic stability. Many of the extant arboreal squirrel-related rodents display a small body size, claws on all digits, and limited prehensility, a combination that was proposed to have characterized the earliest Euarchontoglires. Thus, motion analysis of such a modern analog could shed light onto the early locomotor evolution of eurarchontoglirans. In this study, we investigated how Swinhoe’s striped squirrels (Tamiops swinhoei; Scuiromorpha) adjust their locomotion when faced with different orientations on broad supports and simulated small branches. We simultaneously recorded high-Hz videos (501 trials) and support reaction forces (451 trials) of squirrels running on two types of instrumented trackways installed at either a 45° incline (we recorded locomotion on inclines and declines) or with a horizontal orientation. The striped squirrels almost exclusively used asymmetrical gaits with a preference for full bounds. Locomotion on simulated branches did not differ substantially from locomotion on the flat trackway. We interpreted several of the quantified adjustments on declines and inclines (in comparison to horizontal supports) as mechanisms to increase stability (e.g., by minimizing toppling moments) and as adjustments to the differential loading of fore- and hind limbs on inclined supports. Our data, in addition to published comparative data and similarities to the locomotion of other small arboreal rodents, tree shrews, and primates as well as a likely small body size at the crown-group node of Euarchontoglires, render a preference for asymmetrical gaits in early members of the clade plausible. This contributes to our understanding of the ancestral lifestyle of this mammalian ‘superclade’.
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12
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Nishimaki T, Sato K. P*R*O*P: a web application to perform phylogenetic analysis considering the effect of gaps. BMC Bioinformatics 2021; 22:36. [PMID: 33516169 PMCID: PMC7847139 DOI: 10.1186/s12859-021-03978-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/21/2021] [Indexed: 11/27/2022] Open
Abstract
Background Phylogenetic analysis strongly depends on evolutionary models. Most evolutionary models for estimating genetic differences and phylogenetic relationships do not treat gap sites in the alignment of sequences. Appropriately incorporating evolutionary information of sites containing insertions and deletions into genetic difference measures will be improve the accuracy of phylogenetic estimates. Results We introduced a new measure for estimating genetic differences, and presented P*R*O*P, a web application for performing phylogenetic analysis based on genetic difference considering the effect of gaps. As an example of phylogenetic analysis using P*R*O*P, we used complete p53 amino acid sequences of 31 organisms and illustrated that the genetic differences with and without information on sites containing gaps result in trees with different topologies. Conclusions P*R*O*P is available at https://www.rs.tus.ac.jp/bioinformatics/prop and the user can perform phylogenetic analysis by uploading sequence data on the website. The most distinctive feature of P*R*O*P is its genetic difference that is estimated without eliminating gap sites for alignment sequences, which helps users detect meaningful difference in an evolutionary process. The source code is available in GitHub: https://github.com/TUS-Satolab/PROP.
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Affiliation(s)
- Takuma Nishimaki
- Department of Information Sciences, Tokyo University of Science, Noda City, Chiba, 278-8510, Japan
| | - Keiko Sato
- Department of Information Sciences, Tokyo University of Science, Noda City, Chiba, 278-8510, Japan.
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13
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Bhagwandin A, Debipersadh U, Kaswera-Kyamakya C, Gilissen E, Rockland KS, Molnár Z, Manger PR. Distribution, number, and certain neurochemical identities of infracortical white matter neurons in the brains of three megachiropteran bat species. J Comp Neurol 2020; 528:3023-3038. [PMID: 32103488 DOI: 10.1002/cne.24894] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/06/2020] [Accepted: 02/24/2020] [Indexed: 12/13/2022]
Abstract
A large population of infracortical white matter neurons, or white matter interstitial cells (WMICs), are found within the subcortical white matter of the mammalian telencephalon. We examined WMICs in three species of megachiropterans, Megaloglossus woermanni, Casinycteris argynnis, and Rousettus aegyptiacus, using immunohistochemical and stereological techniques. Immunostaining for neuronal nuclear marker (NeuN) revealed substantial numbers of WMICs in each species-M. woermanni 124,496 WMICs, C. argynnis 138,458 WMICs, and the larger brained R. aegyptiacus having an estimated WMIC population of 360,503. To examine the range of inhibitory neurochemical types we used antibodies against parvalbumin, calbindin, calretinin, and neural nitric oxide synthase (nNOS). The calbindin and nNOS immunostained neurons were the most commonly observed, while those immunoreactive for calretinin and parvalbumin were sparse. The proportion of WMICs exhibiting inhibitory neurochemical profiles was ~26%, similar to that observed in previously studied primates. While for the most part the WMIC population in the megachiropterans studied was similar to that observed in other mammals, the one feature that differed was the high proportion of WMICs immunoreactive to calbindin, whereas in primates (macaque monkey, lar gibbon and human) the highest proportion of inhibitory WMICs contain calretinin. Interestingly, there appears to be an allometric scaling of WMIC numbers with brain mass. Further quantitative comparative work across more mammalian species will reveal the developmental and evolutionary trends associated with this infrequently studied neuronal population.
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Affiliation(s)
- Adhil Bhagwandin
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Parktown, Johannesburg, South Africa
- Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
| | - Ulsana Debipersadh
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Parktown, Johannesburg, South Africa
| | | | - Emmanuel Gilissen
- Department of African Zoology, Royal Museum for Central Africa, Tervuren, Belgium
- Laboratory of Histology and Neuropathology, Université Libre de Bruxelles, Brussels, Belgium
- Department of Anthropology, University of Arkansas, Fayetteville, Arkansas, USA
| | - Kathleen S Rockland
- Department of Anatomy and Neurobiology, Boston University, School of Medicine, Boston, Massachusetts, USA
| | - Zoltán Molnár
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Paul R Manger
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Parktown, Johannesburg, South Africa
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14
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Ciancio MR, Vieytes EC, Castro MC, Carlini AA. Dental enamel structure in long-nosed armadillos (Xenarthra: Dasypus) and its evolutionary implications. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Most xenarthrans have a reduced and simplified dentition that lacks enamel. However, the presence of prismatic enamel has been recorded in the Eocene armadillos Utaetus buccatus (Euphractinae) and Astegotherium dichotomus (Astegotheriini). Among extant xenarthrans, the occurrence of enamel has been recognized only in the long-nosed armadillo, Dasypus novemcinctus (Dasypodinae), but its microstructure has never been described. In this contribution, we analyse the enamel microstructure in deciduous and permanent teeth of four Dasypus species. In deciduous molariform teeth of some species, we identify an apical cap of vestigial enamel (without crystalline structure), interpreted as an amorphous ameloblastic secretion. In permanent teeth, a thin layer of true enamel is found in the apical portion of unworn molariforms. The enamel is prismatic in D. novemcinctus, but in Dasypus hybridus, Dasypus sabanicola and Dasypus punctatus it is prismless. Taking into account the Eocene species of armadillos, the ancestral condition of enamel in cingulates could have been more complex (as in other placentals) and undergone progressive reduction, as shown in the Dasypus lineage. In light of previous genetic and developmental studies, we review and briefly discuss the processes that can account for the reduction/loss of enamel in extant and extinct armadillos. The retention of enamel and the fact that this genus is the only living xenarthran with two functional generations of teeth support the early divergence of the Dasypus lineage among living cingulates. This is in agreement with morphological and molecular analyses.
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Affiliation(s)
- Martín R Ciancio
- Laboratorio de Morfología Evolutiva y Desarrollo (MORPHOS) y División Paleontología Vertebrados, Museo de La Plata, CONICET, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque s/n, B1900FWA, La Plata, Argentina
- Cátedra Anatomía Comparada, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque s/n, B1900FWA, La Plata, Argentina
| | - Emma C Vieytes
- Cátedra Anatomía Comparada, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque s/n, B1900FWA, La Plata, Argentina
- División Zoología Vertebrados, Museo de La Plata, CONICET, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque s/n, B1900FWA, La Plata, Argentina
| | - Mariela C Castro
- Departamento de Ciências Biológicas, IBiotec, Universidade Federal de Catalão, Avenida Dr. Lamartine Pinto de Avelar, 1120, 75704-020, Catalão, Brazil
| | - Alfredo A Carlini
- Laboratorio de Morfología Evolutiva y Desarrollo (MORPHOS) y División Paleontología Vertebrados, Museo de La Plata, CONICET, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque s/n, B1900FWA, La Plata, Argentina
- Cátedra Anatomía Comparada, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque s/n, B1900FWA, La Plata, Argentina
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15
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López-Torres S, Bertrand OC, Lang MM, Silcox MT, Fostowicz-Frelik Ł. Cranial endocast of the stem lagomorph Megalagus and brain structure of basal Euarchontoglires. Proc Biol Sci 2020; 287:20200665. [PMID: 32576117 PMCID: PMC7329053 DOI: 10.1098/rspb.2020.0665] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Early lagomorphs are central to our understanding of how the brain evolved in Glires (rodents, lagomorphs and their kin) from basal members of Euarchontoglires (Glires + Euarchonta, the latter grouping primates, treeshrews, and colugos). Here, we report the first virtual endocast of the fossil lagomorph Megalagus turgidus, from the Orella Member of the Brule Formation, early Oligocene, Nebraska, USA. The specimen represents one of the oldest nearly complete lagomorph skulls known. Primitive aspects of the endocranial morphology in Megalagus include large olfactory bulbs, exposure of the midbrain, a small neocortex and a relatively low encephalization quotient. Overall, this suggests a brain morphology closer to that of other basal members of Euarchontoglires (e.g. plesiadapiforms and ischyromyid rodents) than to that of living lagomorphs. However, the well-developed petrosal lobules in Megalagus, comparable to the condition in modern lagomorphs, suggest early specialization in that order for the stabilization of eye movements necessary for accurate visual tracking. Our study sheds new light on the reconstructed morphology of the ancestral brain in Euarchontoglires and fills a critical gap in the understanding of palaeoneuroanatomy of this major group of placental mammals.
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Affiliation(s)
- Sergi López-Torres
- Division of Paleontology, American Museum of Natural History, New York, NY, USA.,Richard Gilder Graduate School, American Museum of Natural History, New York, NY, USA.,New York Consortium in Evolutionary Primatology, New York, NY, USA.,Department of Evolutionary Paleobiology, Institute of Paleobiology, Polish Academy of Sciences, Warsaw, Poland
| | - Ornella C Bertrand
- School of Geosciences, Grant Institute, University of Edinburgh, Edinburgh EH9 3FE, UK
| | - Madlen M Lang
- Department of Anthropology, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Mary T Silcox
- Department of Anthropology, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Łucja Fostowicz-Frelik
- Department of Evolutionary Paleobiology, Institute of Paleobiology, Polish Academy of Sciences, Warsaw, Poland.,Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, People's Republic of China
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16
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Rotwein P, Baral K. Zmat2 in mammals: conservation and diversification among genes and Pseudogenes. BMC Genomics 2020; 21:113. [PMID: 32005145 PMCID: PMC6995233 DOI: 10.1186/s12864-020-6506-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/17/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Recent advances in genetics and genomics present unique opportunities for enhancing our understanding of mammalian biology and evolution through detailed multi-species comparative analysis of gene organization and expression. Yet, of the more than 20,000 protein coding genes found in mammalian genomes, fewer than 10% have been examined in any detail. Here we elucidate the power of data available in publicly-accessible genomic and genetic resources by querying them to evaluate Zmat2, a minimally studied gene whose human ortholog has been implicated in spliceosome function and in keratinocyte differentiation. RESULTS We find extensive conservation in coding regions and overall structure of Zmat2 in 18 mammals representing 13 orders and spanning ~ 165 million years of evolutionary development, and in their encoded proteins. We identify a tandem duplication in the Zmat2 gene and locus in opossum, but not in other monotremes, marsupials, or other mammals, indicating that this event occurred subsequent to the divergence of these species from one another. We also define a collection of Zmat2 pseudogenes in half of the mammals studied, and suggest based on phylogenetic analysis that they each arose independently in the recent evolutionary past. CONCLUSIONS Mammalian Zmat2 genes and ZMAT2 proteins illustrate conservation of structure and sequence, along with the development and diversification of pseudogenes in a large fraction of species. Collectively, these observations also illustrate how the focused identification and interpretation of data found in public genomic and gene expression resources can be leveraged to reveal new insights of potentially high biological significance.
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Affiliation(s)
- Peter Rotwein
- Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech Health University Health Sciences Center, El Paso, TX, 79905, USA.
| | - Kabita Baral
- Graduate School, College of Science, University of Texas at El Paso, El Paso, TX, 79902, USA
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17
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Rossi LF, Nottola S, Miglietta S, Macchiarelli G, Luaces JP, Merico V, Merani S, Garagna S, Zuccotti M. Germ cell cysts, a fetal feature in mammals, are constitutively present in the adult armadillo. Mol Reprod Dev 2019; 87:91-101. [DOI: 10.1002/mrd.23296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/30/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Luis Francisco Rossi
- Laboratorio de Biología Cromosómica, Facultad de MedicinaUniversidad de Buenos AiresBuenos Aires Argentina
- Consejo Nacional de Investigaciones Científicas y TécnicasBuenos Aires Argentina
| | - Stefania Nottola
- Department of Anatomy, Histology, Forensic Medicine and OrthopedicsUniversity of Rome La SapienzaRome Italy
| | - Selenia Miglietta
- Department of Anatomy, Histology, Forensic Medicine and OrthopedicsUniversity of Rome La SapienzaRome Italy
| | - Guido Macchiarelli
- Department of Life, Health and Environmental SciencesUniversity of L'aquilaL'aquila Italy
| | - Juan Pablo Luaces
- Laboratorio de Biología Cromosómica, Facultad de MedicinaUniversidad de Buenos AiresBuenos Aires Argentina
- Consejo Nacional de Investigaciones Científicas y TécnicasBuenos Aires Argentina
| | - Valeria Merico
- Department of Biology and Biotechnology “Lazzaro Spallanzani,”University of PaviaPavia Italy
- Centre for Health TechnologyUniversity of PaviaPavia Italy
| | - Susana Merani
- Laboratorio de Biología Cromosómica, Facultad de MedicinaUniversidad de Buenos AiresBuenos Aires Argentina
- Consejo Nacional de Investigaciones Científicas y TécnicasBuenos Aires Argentina
| | - Silvia Garagna
- Department of Biology and Biotechnology “Lazzaro Spallanzani,”University of PaviaPavia Italy
- Centre for Health TechnologyUniversity of PaviaPavia Italy
| | - Maurizio Zuccotti
- Department of Biology and Biotechnology “Lazzaro Spallanzani,”University of PaviaPavia Italy
- Centre for Health TechnologyUniversity of PaviaPavia Italy
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18
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Mynhardt S, Bennett NC, Bloomer P. New insights from RADseq data on differentiation in the Hottentot golden mole species complex from South Africa. Mol Phylogenet Evol 2019; 143:106667. [PMID: 31676418 DOI: 10.1016/j.ympev.2019.106667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 10/28/2019] [Accepted: 10/28/2019] [Indexed: 10/25/2022]
Abstract
Golden moles (Family Chrysochloridae) are small subterranean mammals, endemic to sub-Saharan Africa, and many of the 21 species are listed as threatened on the IUCN Red List. Most species have highly restricted ranges; however two species, the Hottentot golden mole (Amblysomus hottentotus) and the Cape golden mole (Chrysochloris asiatica) have relatively wide ranges. We recently uncovered cryptic diversity within A. hottentotus, through a phylogeographic analysis of this taxon using two mitochondrial gene regions and a nuclear intron. To further investigate this cryptic diversity, we generated nuclear SNP data from across the genome of A. hottentotus, by means of double-digest restriction-site associated DNA sequencing (ddRADSeq), and mapped reads to the Cape golden mole genome. We conducted a phylogenetic analysis and investigated population differentiation. Our results support the distinctiveness of A. h. meesteri. Furthermore, we provide evidence from nuclear SNPs in support of our previous finding that Central coastal samples represent a unique cryptic lineage that is highly divergent from A. h. pondoliae farther south. Although mtDNA suggests that Umtata may represent a unique lineage sister to A. h. longiceps, mito-nuclear discordance from our RADseq data indicate that these samples may instead be closer to A. h. pondoliae, and therefore may not represent a distinct lineage. We stress the importance of recognizing that understudied populations, such as that of Umtata, may represent populations or ESUs under threat and in need of conservation attention. We present a high-quality filtered SNP dataset, comprising thousands of SNPs, which may serve as a useful resource for future golden mole studies. We have thus added to the growing body of research demonstrating the power and utility of RADseq to investigate population differentiation.
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Affiliation(s)
- Samantha Mynhardt
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa; Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa.
| | - Nigel C Bennett
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa; Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa.
| | - Paulette Bloomer
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa; Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa.
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19
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Baral K, Rotwein P. The insulin-like growth factor 2 gene in mammals: Organizational complexity within a conserved locus. PLoS One 2019; 14:e0219155. [PMID: 31251794 PMCID: PMC6599137 DOI: 10.1371/journal.pone.0219155] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/17/2019] [Indexed: 01/10/2023] Open
Abstract
The secreted protein, insulin-like growth factor 2 (IGF2), plays a central role in fetal and prenatal growth and development, and is regulated at the genetic level by parental imprinting, being expressed predominantly from the paternally derived chromosome in mice and humans. Here, IGF2/Igf2 and its locus has been examined in 19 mammals from 13 orders spanning ~166 million years of evolutionary development. By using human or mouse DNA segments as queries in genome analyses, and by assessing gene expression using RNA-sequencing libraries, more complexity was identified within IGF2/Igf2 than was annotated previously. Multiple potential 5’ non-coding exons were mapped in most mammals and are presumably linked to distinct IGF2/Igf2 promoters, as shown for several species by interrogating RNA-sequencing libraries. DNA similarity was highest in IGF2/Igf2 coding exons; yet, even though the mature IGF2 protein was conserved, versions of 67 or 70 residues are produced secondary to species-specific maintenance of alternative RNA splicing at a variable intron-exon junction. Adjacent H19 was more divergent than IGF2/Igf2, as expected in a gene for a noncoding RNA, and was identified in only 10/19 species. These results show that common features, including those defining IGF2/Igf2 coding and several non-coding exons, were likely present at the onset of the mammalian radiation, but that others, such as a putative imprinting control region 5’ to H19 and potential enhancer elements 3’ to H19, diversified with speciation. This study also demonstrates that careful analysis of genomic and gene expression repositories can provide new insights into gene structure and regulation.
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Affiliation(s)
- Kabita Baral
- Graduate School, College of Science, University of Texas at El Paso, El Paso, Texas
| | - Peter Rotwein
- Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech Health University Health Sciences Center, El Paso, Texas
- * E-mail:
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Nyakatura JA. Early primate evolution: insights into the functional significance of grasping from motion analyses of extant mammals. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- John A Nyakatura
- AG Morphologie und Formengeschichte, Institut für Biologie, Humboldt Universität, Philippstraße, Berlin, Germany
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Williams SA, Spear JK, Petrullo L, Goldstein DM, Lee AB, Peterson AL, Miano DA, Kaczmarek EB, Shattuck MR. Increased variation in numbers of presacral vertebrae in suspensory mammals. Nat Ecol Evol 2019; 3:949-956. [DOI: 10.1038/s41559-019-0894-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 04/08/2019] [Indexed: 11/09/2022]
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Beck RMD, Baillie C. Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny. Proc Biol Sci 2018; 285:20181632. [PMID: 30963896 PMCID: PMC6304057 DOI: 10.1098/rspb.2018.1632] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/23/2018] [Indexed: 01/16/2023] Open
Abstract
Phylogenies of mammals based on morphological data continue to show several major areas of conflict with the current consensus view of their relationships, which is based largely on molecular data. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships. We tested this under a hypothetical 'best case scenario' by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive DNA sequence-based phylogeny of mammals, and then seeing what effect the subsequent inclusion of these predicted ancestors had on unconstrained phylogenetic analyses of morphological data. We found that this resulted in topologies that are highly congruent with the current consensus phylogeny, at least when the predicted ancestors are assumed to be well preserved and densely sampled. Most strikingly, several analyses recovered the monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record-specifically the discovery of fossil taxa that preserve the ancestral or near-ancestral morphologies of the nodes in the current consensus-may be sufficient to largely reconcile morphological and molecular estimates of mammal phylogeny, even using current morphological character sets.
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Affiliation(s)
- Robin M. D. Beck
- School of Environment and Life Sciences, University of Salford, Manchester M5 4WT, UK
| | - Charles Baillie
- School of Environment and Life Sciences, University of Salford, Manchester M5 4WT, UK
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Montañez‐Rivera I, Nyakatura JA, Amson E. Bone cortical compactness in 'tree sloths' reflects convergent evolution. J Anat 2018; 233:580-591. [PMID: 30117161 PMCID: PMC6183012 DOI: 10.1111/joa.12873] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2018] [Indexed: 01/15/2023] Open
Abstract
Bone remodeling, one of the main processes that regulate bone microstructure, consists of bone resorption followed by the deposition of secondary bone at the same location. Remodeling intensity varies among taxa, but a characteristically compact cortex is ubiquitous in the long bones of mature terrestrial mammals. A previous analysis found that cortical bone in a few 'tree sloth' (Bradypus and Choloepus) specimens is heavily remodeled and characterized by numerous immature secondary osteons, suggesting that these animals were remodeling their bones at high rate until late in their ontogeny. This study aims at testing if this remodeling is generally present in 'tree sloths', using a quantitative analysis of the humeral cortical compactness (CC) among xenarthrans. The results of the investigation of humeral diaphyseal cross-sections of 26 specimens belonging to 10 xenarthran species including specimens from both extinct and extant species indicate that in 'tree sloths' the CC is significantly lower than in the other sampled xenarthrans. No significant difference was found between the CC of the two genera of 'tree sloths'. Our results are consistent with the hypothesis that the cortical bone of 'tree sloths' in general undergoes intense and balanced remodeling that is maintained until late (possibly throughout) in their ontogeny. In the light of xenarthran phylogeny, low CC represents another convergence between the long-separated 'tree sloth' lineages. Although the exact structural and/or functional demands that are associated with this trait are hitherto unknown, several hypotheses are suggested here, including a relationship to their relatively low metabolism and to the mechanical demands imposed upon the bones by the suspensory posture and locomotion, which was independently acquired by the two genera of 'tree sloths'.
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Affiliation(s)
- Irene Montañez‐Rivera
- AG Morphologie und FormengeschichteInstitut für BiologieHumboldt UniversitätBerlinGermany
| | - John A. Nyakatura
- AG Morphologie und FormengeschichteInstitut für BiologieHumboldt UniversitätBerlinGermany
- Bild Wissen Gestaltung. Ein interdisziplinäres LaborHumboldt UniversitätBerlinGermany
| | - Eli Amson
- AG Morphologie und FormengeschichteInstitut für BiologieHumboldt UniversitätBerlinGermany
- Bild Wissen Gestaltung. Ein interdisziplinäres LaborHumboldt UniversitätBerlinGermany
- Museum für NaturkundeLeibniz‐Institut für Evolutions‐ und BiodiversitätsforschungBerlinGermany
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Washausen S, Scheffel T, Brunnett G, Knabe W. Possibilities and limitations of three-dimensional reconstruction and simulation techniques to identify patterns, rhythms and functions of apoptosis in the early developing neural tube. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2018; 40:55. [PMID: 30159859 DOI: 10.1007/s40656-018-0222-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/19/2018] [Indexed: 06/08/2023]
Abstract
The now classical idea that programmed cell death (apoptosis) contributes to a plethora of developmental processes still has lost nothing of its impact. It is, therefore, important to establish effective three-dimensional (3D) reconstruction as well as simulation techniques to decipher the exact patterns and functions of such apoptotic events. The present study focuses on the question whether and how apoptosis promotes neurulation-associated processes in the spinal cord of Tupaia belangeri (Tupaiidae, Scandentia, Mammalia). Our 3D reconstructions demonstrate that at least two craniocaudal waves of apoptosis consecutively pass through the dorsal spinal cord. The first wave appears to be involved in neural fold fusion and/or in selection processes among premigratory neural crest cells. The second one seems to assist in establishing the dorsal signaling center known as the roof plate. In the hindbrain, in contrast, apoptosis among premigratory neural crest cells progresses craniocaudally but discontinuously, in a segment-specific manner. Unlike apoptosis in the spinal cord, these segment-specific apoptotic events, however, precede later ones that seemingly support neural fold fusion and/or postfusion remodeling. Arguing with Whitehead that biological patterns and rhythms differ in that biological rhythms depend "upon the differences involved in each exhibition of the pattern" (Whitehead in An enquiry concerning the principles of natural knowledge. Cambridge University Press, London, 1919, p. 198) we show that 3D reconstruction and simulation techniques can contribute to distinguish between (static) patterns and (dynamic) rhythms of apoptosis. By deciphering novel patterns and rhythms of developmental apoptosis, our reconstructions help to reconcile seemingly inconsistent earlier findings in chick and mouse embryos, and to create rules for computer simulations.
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Affiliation(s)
- Stefan Washausen
- Department Prosektur Anatomie, Westfälische Wilhelms-University, Vesaliusweg 2-4, 48149, Münster, Germany
| | - Thomas Scheffel
- Department of Psychiatry, Psychotherapy and Psychosomatics, Brandenburg Medical School, Campus Neuruppin, 16816, Neuruppin, Germany
| | - Guido Brunnett
- Department of Informatics, Technical University, 09107, Chemnitz, Germany
| | - Wolfgang Knabe
- Department Prosektur Anatomie, Westfälische Wilhelms-University, Vesaliusweg 2-4, 48149, Münster, Germany.
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Sharma V, Lehmann T, Stuckas H, Funke L, Hiller M. Loss of RXFP2 and INSL3 genes in Afrotheria shows that testicular descent is the ancestral condition in placental mammals. PLoS Biol 2018; 16:e2005293. [PMID: 29953435 PMCID: PMC6023123 DOI: 10.1371/journal.pbio.2005293] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 05/24/2018] [Indexed: 01/13/2023] Open
Abstract
Descent of testes from a position near the kidneys into the lower abdomen or into the scrotum is an important developmental process that occurs in all placental mammals, with the exception of five afrotherian lineages. Since soft-tissue structures like testes are not preserved in the fossil record and since key parts of the placental mammal phylogeny remain controversial, it has been debated whether testicular descent is the ancestral or derived condition in placental mammals. To resolve this debate, we used genomic data of 71 mammalian species and analyzed the evolution of two key genes (relaxin/insulin-like family peptide receptor 2 [RXFP2] and insulin-like 3 [INSL3]) that induce the development of the gubernaculum, the ligament that is crucial for testicular descent. We show that both RXFP2 and INSL3 are lost or nonfunctional exclusively in four afrotherians (tenrec, cape elephant shrew, cape golden mole, and manatee) that completely lack testicular descent. The presence of remnants of once functional orthologs of both genes in these afrotherian species shows that these gene losses happened after the split from the placental mammal ancestor. These “molecular vestiges” provide strong evidence that testicular descent is the ancestral condition, irrespective of persisting phylogenetic discrepancies. Furthermore, the absence of shared gene-inactivating mutations and our estimates that the loss of RXFP2 happened at different time points strongly suggest that testicular descent was lost independently in Afrotheria. Our results provide a molecular mechanism that explains the loss of testicular descent in afrotherians and, more generally, highlight how molecular vestiges can provide insights into the evolution of soft-tissue characters. While fossils of whales with legs demonstrate that these species evolved from legged ancestors, the ancestral state of nonfossilizing soft-tissue structures can only be indirectly inferred. This difficulty is also confounded by uncertainties in the phylogenetic relationships between the animals concerned. A prime example is the case of testicular descent, a developmental process that determines the final position of testes, which occurs in most placental mammals but is absent from several afrotherian lineages. Here, we discovered that afrotherians possess remnants of genes known to be required for testicular descent. These “molecular vestiges” show that testicular descent was already present in the placental ancestor and was subsequently lost in Afrotheria. Our study highlights the potential of molecular vestiges in resolving contradictory ancestral states of soft-tissue characters.
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Affiliation(s)
- Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Center for Systems Biology Dresden, Germany
| | - Thomas Lehmann
- Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
| | | | - Liane Funke
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Center for Systems Biology Dresden, Germany
- * E-mail:
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Hautier L, Oliver JD, Pierce SE. An Overview of Xenarthran Developmental Studies with a Focus on the Development of the Xenarthrous Vertebrae. J MAMM EVOL 2017. [DOI: 10.1007/s10914-017-9412-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary. Proc Natl Acad Sci U S A 2017; 114:E7282-E7290. [PMID: 28808022 DOI: 10.1073/pnas.1616744114] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The timing of the diversification of placental mammals relative to the Cretaceous-Paleogene (KPg) boundary mass extinction remains highly controversial. In particular, there have been seemingly irreconcilable differences in the dating of the early placental radiation not only between fossil-based and molecular datasets but also among molecular datasets. To help resolve this discrepancy, we performed genome-scale analyses using 4,388 loci from 90 taxa, including representatives of all extant placental orders and transcriptome data from flying lemurs (Dermoptera) and pangolins (Pholidota). Depending on the gene partitioning scheme, molecular clock model, and genic deviation from molecular clock assumptions, extensive sensitivity analyses recovered widely varying diversification scenarios for placental mammals from a given gene set, ranging from a deep Cretaceous origin and diversification to a scenario spanning the KPg boundary, suggesting that the use of suboptimal molecular clock markers and methodologies is a major cause of controversies regarding placental diversification timing. We demonstrate that reconciliation between molecular and paleontological estimates of placental divergence times can be achieved using the appropriate clock model and gene partitioning scheme while accounting for the degree to which individual genes violate molecular clock assumptions. A birth-death-shift analysis suggests that placental mammals underwent a continuous radiation across the KPg boundary without apparent interruption by the mass extinction, paralleling a genus-level radiation of multituberculates and ecomorphological diversification of both multituberculates and therians. These findings suggest that the KPg catastrophe evidently played a limited role in placental diversification, which, instead, was likely a delayed response to the slightly earlier radiation of angiosperms.
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Internal Morphology of Osteoderms of Extinct Armadillos and Its Relationship with Environmental Conditions. J MAMM EVOL 2017. [DOI: 10.1007/s10914-017-9404-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Advantages and Limitations in the Use of Extant Xenarthrans (Mammalia) as Morphological Models for Paleobiological Reconstruction. J MAMM EVOL 2017. [DOI: 10.1007/s10914-017-9400-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Feijoo M, Parada A. Macrosystematics of eutherian mammals combining HTS data to expand taxon coverage. Mol Phylogenet Evol 2017; 113:76-83. [PMID: 28487261 DOI: 10.1016/j.ympev.2017.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 05/04/2017] [Accepted: 05/04/2017] [Indexed: 02/04/2023]
Abstract
In the last few years high-throughput sequencing technologies have permitted significant advances in mammalian phylogenetic studies from a genomic perspective. However, these studies have been restricted to a sparse number of species with available reference genomes. Thus, several issues inside the eutherian mammals phylogeny remain unresolved. This may be due in part to limited taxon sampling, as taxonomic density is known to affect phylogenetic resolution. In this context, we present a protocol to increase taxon coverage using high-throughput sequencing data (RNA or DNA) generated for other biological studies and available in public databases. Following this procedure we addressed pending or controversial issues concerning the phylogenetic position of Dermoptera, Pholidota and Chiroptera, considering multiple and independent loci. Also for Chiroptera and Arctoidea we evaluated the relationships of the lineages that compose it. Although the maximum number of genes used is moderate (95), in some cases taxon coverage doubles that of previous related studies. Globally, all coalescent-based (STAR, MP-EST and ASTRAL) and concatenated (IQ-TREE and BEAST2) methods used for species tree reconstruction were consistent to each other and most of interrogated nodes received high statistical support.
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Affiliation(s)
- M Feijoo
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo CP 11400, Uruguay.
| | - A Parada
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia CP 5090000, Chile.
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Sánchez-Villagra MR, Forasiepi AM. On the development of the chondrocranium and the histological anatomy of the head in perinatal stages of marsupial mammals. ZOOLOGICAL LETTERS 2017; 3:1. [PMID: 28203388 PMCID: PMC5303607 DOI: 10.1186/s40851-017-0062-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 02/07/2017] [Indexed: 05/06/2023]
Abstract
An overview of the literature on the chondrocranium of marsupial mammals reveals a relative conservatism in shape and structures. We document the histological cranial anatomy of individuals representing Monodelphis domestica, Dromiciops gliroides, Perameles sp. and Macropus eugenii. The marsupial chondrocranium is generally characterized by the great breadth of the lamina basalis, absence of pila metoptica and large otic capsules. Its most anterior portion (cupula nasi anterior) is robust, and anterior to it there are well-developed tactile sensory structures, functionally important in the neonate. Investigations of ossification centers at and around the nasal septum are needed to trace the presence of certain bones (e.g., mesethmoid, parasphenoid) across marsupial taxa. In many adult marsupials, the tympanic floor is formed by at least three bones: alisphenoid (alisphenoid tympanic process), ectotympanic and petrosal (rostral and caudal tympanic processes); the squamosal also contributes in some diprotodontians. The presence of an entotympanic in marsupials has not been convincingly demonstrated. The tubal element surrounding the auditory tube in most marsupials is fibrous connective tissue rather than cartilage; the latter is the case in most placentals recorded to date. However, we detected fibrocartilage in a late juvenile of Dromiciops, and a similar tissue has been reported for Tarsipes. Contradictory reports on the presence of the tegmen tympani can be found in the literature. We describe a small tegmen tympani in Macropus. Several heterochronic shifts in the timing of development of the chondocranium and associated structures (e.g., nerves, muscles) and in the ossification sequence have been interpreted as largely being influenced by functional requirements related to the altriciality of the newborn marsupial during early postnatal life. Comparative studies of chondocranial development of mammals can benefit from a solid phylogenetic framework, research on non-classical model organisms, and integration with imaging and sectional data derived from computer-tomography.
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Affiliation(s)
- Marcelo R. Sánchez-Villagra
- Paläontologisches Institut und Museum der Universität Zürich, Karl Schmid Strasse 4, Zürich, 8006 Switzerland
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Coley JD, Arenson M, Xu Y, Tanner KD. Intuitive biological thought: Developmental changes and effects of biology education in late adolescence. Cogn Psychol 2017; 92:1-21. [DOI: 10.1016/j.cogpsych.2016.11.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 11/01/2016] [Accepted: 11/01/2016] [Indexed: 10/20/2022]
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Reyes LD, Harland T, Reep RL, Sherwood CC, Jacobs B. Golgi Analysis of Neuron Morphology in the Presumptive Somatosensory Cortex and Visual Cortex of the Florida Manatee (Trichechus manatus latirostris). BRAIN, BEHAVIOR AND EVOLUTION 2016; 87:105-16. [PMID: 27166161 DOI: 10.1159/000445495] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/15/2016] [Indexed: 11/19/2022]
Abstract
The current study investigates neuron morphology in presumptive primary somatosensory (S1) and primary visual (V1) cortices of the Florida manatee (Trichechus manatus latirostris) as revealed by Golgi impregnation. Sirenians, including manatees, have an aquatic lifestyle, a large body size, and a relatively large lissencephalic brain. The present study examines neuron morphology in 3 cortical areas: in S1, dorsolateral cortex area 1 (DL1) and cluster cortex area 2 (CL2) and in V1, dorsolateral cortex area 4 (DL4). Neurons exhibited a variety of morphological types, with pyramidal neurons being the most common. The large variety of neuron types present in the manatee cortex was comparable to that seen in other eutherian mammals, except for rodents and primates, where pyramid-shaped neurons predominate. A comparison between pyramidal neurons in S1 and V1 indicated relatively greater dendritic branching in S1. Across all 3 areas, the dendritic arborization pattern of pyramidal neurons was also similar to that observed previously in the afrotherian rock hyrax, cetartiodactyls, opossums, and echidnas but did not resemble the widely bifurcated dendrites seen in the large-brained African elephant. Despite adaptations for an aquatic environment, manatees did not share specific neuron types such as tritufted and star-like neurons that have been found in cetaceans. Manatees exhibit an evolutionarily primitive pattern of cortical neuron morphology shared with most other mammals and do not appear to have neuronal specializations for an aquatic niche.
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Affiliation(s)
- Laura D Reyes
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, D.C., USA
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Buckley M. Ancient collagen reveals evolutionary history of the endemic South American 'ungulates'. Proc Biol Sci 2016; 282:20142671. [PMID: 25833851 PMCID: PMC4426609 DOI: 10.1098/rspb.2014.2671] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Since the late eighteenth century, fossils of bizarre extinct creatures have been described from the Americas, revealing a previously unimagined chapter in the history of mammals. The most bizarre of these are the ‘native’ South American ungulates thought to represent a group of mammals that evolved in relative isolation on South America, but with an uncertain affinity to any particular placental lineage. Many authors have considered them descended from Laurasian ‘condylarths’, which also includes the probable ancestors of perissodactyls and artiodactyls, whereas others have placed them either closer to the uniquely South American xenarthrans (anteaters, armadillos and sloths) or the basal afrotherians (e.g. elephants and hyraxes). These hypotheses have been debated owing to conflicting morphological characteristics and the hitherto inability to retrieve molecular information. Of the ‘native’ South American mammals, only the toxodonts and litopterns persisted until the Late Pleistocene–Early Holocene. Owing to known difficulties in retrieving ancient DNA (aDNA) from specimens from warm climates, this research presents a molecular phylogeny for both Macrauchenia patachonica (Litopterna) and Toxodon platensis (Notoungulata) recovered using proteomics-based (liquid chromatography–tandem mass spectrometry) sequencing analyses of bone collagen. The results place both taxa in a clade that is monophyletic with the perissodactyls, which today are represented by horses, rhinoceroses and tapirs.
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Affiliation(s)
- Michael Buckley
- Faculty of Life Sciences, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
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Reyes LD, Stimpson CD, Gupta K, Raghanti MA, Hof PR, Reep RL, Sherwood CC. Neuron Types in the Presumptive Primary Somatosensory Cortex of the Florida Manatee (Trichechus manatus latirostris). BRAIN, BEHAVIOR AND EVOLUTION 2015; 86:210-31. [PMID: 26613530 DOI: 10.1159/000441964] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 10/25/2015] [Indexed: 11/19/2022]
Abstract
Within afrotherians, sirenians are unusual due to their aquatic lifestyle, large body size and relatively large lissencephalic brain. However, little is known about the neuron type distributions of the cerebral cortex in sirenians within the context of other afrotherians and aquatic mammals. The present study investigated two cortical regions, dorsolateral cortex area 1 (DL1) and cluster cortex area 2 (CL2), in the presumptive primary somatosensory cortex (S1) in Florida manatees (Trichechus manatus latirostris) to characterize cyto- and chemoarchitecture. The mean neuron density for both cortical regions was 35,617 neurons/mm(3) and fell within the 95% prediction intervals relative to brain mass based on a reference group of afrotherians and xenarthrans. Densities of inhibitory interneuron subtypes labeled against calcium-binding proteins and neuropeptide Y were relatively low compared to afrotherians and xenarthrans and also formed a small percentage of the overall population of inhibitory interneurons as revealed by GAD67 immunoreactivity. Nonphosphorylated neurofilament protein-immunoreactive (NPNFP-ir) neurons comprised a mean of 60% of neurons in layer V across DL1 and CL2. DL1 contained a higher percentage of NPNFP-ir neurons than CL2, although CL2 had a higher variety of morphological types. The mean percentage of NPNFP-ir neurons in the two regions of the presumptive S1 were low compared to other afrotherians and xenarthrans but were within the 95% prediction intervals relative to brain mass, and their morphologies were comparable to those found in other afrotherians and xenarthrans. Although this specific pattern of neuron types and densities sets the manatee apart from other afrotherians and xenarthrans, the manatee isocortex does not appear to be explicitly adapted for an aquatic habitat. Many of the features that are shared between manatees and cetaceans are also shared with a diverse array of terrestrial mammals and likely represent highly conserved neural features. A comparative study across manatees and dugongs is necessary to determine whether these traits are specific to one or more of the manatee species, or can be generalized to all sirenians.
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Affiliation(s)
- Laura D Reyes
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, D.C., USA
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Beck RMD, Lee MSY. Ancient dates or accelerated rates? Morphological clocks and the antiquity of placental mammals. Proc Biol Sci 2015; 281:rspb.2014.1278. [PMID: 25165770 DOI: 10.1098/rspb.2014.1278] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Analyses of a comprehensive morphological character matrix of mammals using 'relaxed' clock models (which simultaneously estimate topology, divergence dates and evolutionary rates), either alone or in combination with an 8.5 kb nuclear sequence dataset, retrieve implausibly ancient, Late Jurassic-Early Cretaceous estimates for the initial diversification of Placentalia (crown-group Eutheria). These dates are much older than all recent molecular and palaeontological estimates. They are recovered using two very different clock models, and regardless of whether the tree topology is freely estimated or constrained using scaffolds to match the current consensus placental phylogeny. This raises the possibility that divergence dates have been overestimated in previous analyses that have applied such clock models to morphological and total evidence datasets. Enforcing additional age constraints on selected internal divergences results in only a slight reduction of the age of Placentalia. Constraining Placentalia to less than 93.8 Ma, congruent with recent molecular estimates, does not require major changes in morphological or molecular evolutionary rates. Even constraining Placentalia to less than 66 Ma to match the 'explosive' palaeontological model results in only a 10- to 20-fold increase in maximum evolutionary rate for morphology, and fivefold for molecules. The large discrepancies between clock- and fossil-based estimates for divergence dates might therefore be attributable to relatively small changes in evolutionary rates through time, although other explanations (such as overly simplistic models of morphological evolution) need to be investigated. Conversely, dates inferred using relaxed clock models (especially with discrete morphological data and MrBayes) should be treated cautiously, as relatively minor deviations in rate patterns can generate large effects on estimated divergence dates.
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Affiliation(s)
- Robin M D Beck
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Michael S Y Lee
- School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia Earth Sciences Section, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
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Bianchetti L, Tarabay Y, Lecompte O, Stote R, Poch O, Dejaegere A, Viville S. Tex19 and Sectm1 concordant molecular phylogenies support co-evolution of both eutherian-specific genes. BMC Evol Biol 2015; 15:222. [PMID: 26459560 PMCID: PMC4603632 DOI: 10.1186/s12862-015-0506-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 10/01/2015] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Transposable elements (TE) have attracted much attention since they shape the genome and contribute to species evolution. Organisms have evolved mechanisms to control TE activity. Testis expressed 19 (Tex19) represses TE expression in mouse testis and placenta. In the human and mouse genomes, Tex19 and Secreted and transmembrane 1 (Sectm1) are neighbors but are not homologs. Sectm1 is involved in immunity and its molecular phylogeny is unknown. METHODS Using multiple alignments of complete protein sequences (MACS), we inferred Tex19 and Sectm1 molecular phylogenies. Protein conserved regions were identified and folds were predicted. Finally, expression patterns were studied across tissues and species using RNA-seq public data and RT-PCR. RESULTS We present 2 high quality alignments of 58 Tex19 and 58 Sectm1 protein sequences from 48 organisms. First, both genes are eutherian-specific, i.e., exclusively present in mammals except monotremes (platypus) and marsupials. Second, Tex19 and Sectm1 have both duplicated in Sciurognathi and Bovidae while they have remained as single copy genes in all further placental mammals. Phylogenetic concordance between both genes was significant (p-value < 0.05) and supported co-evolution and functional relationship. At the protein level, Tex19 exhibits 3 conserved regions and 4 invariant cysteines. In particular, a CXXC motif is present in the N-terminal conserved region. Sectm1 exhibits 2 invariant cysteines and an Ig-like domain. Strikingly, Tex19 C-terminal conserved region was lost in Haplorrhini primates while a Sectm1 C-terminal extra domain was acquired. Finally, we have determined that Tex19 and Sectm1 expression levels anti-correlate across the testis of several primates (ρ = -0.72) which supports anti-regulation. CONCLUSIONS Tex19 and Sectm1 co-evolution and anti-regulated expressions support a strong functional relationship between both genes. Since Tex19 operates a control on TE and Sectm1 plays a role in immunity, Tex19 might suppress an immune response directed against cells that show TE activity in eutherian reproductive tissues.
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Affiliation(s)
- Laurent Bianchetti
- Biocomputing and Molecular Modelling Laboratory, Integrated Structural Biology Department, Genetics institute of Molecular and Cellular Biology (IGBMC), INSERM U964/CNRS UMR 1704/Strasbourg University, 1 rue Laurent Fries, 67404, Illkirch, France.
| | - Yara Tarabay
- Primordial Germ Cells' Ontogeny and Pluripotency Laboratory, Functional Genomics and Cancer Department, Genetics Institute of Molecular and Cellular Biology (IGBMC), INSERM U964/CNRS UMR 1704/Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France. .,Present address: Institut de génétique humaine (IGH), 141 rue de la Cardonille, 34396, Montpellier, France.
| | - Odile Lecompte
- Bioinformatics and Integrated Genomics Laboratory (LBGI), ICube, CNRS UMR 7357/Université de Strasbourg, 11 rue Humann, 67085, Strasbourg, France.
| | - Roland Stote
- Biocomputing and Molecular Modelling Laboratory, Integrated Structural Biology Department, Genetics institute of Molecular and Cellular Biology (IGBMC), INSERM U964/CNRS UMR 1704/Strasbourg University, 1 rue Laurent Fries, 67404, Illkirch, France.
| | - Olivier Poch
- Bioinformatics and Integrated Genomics Laboratory (LBGI), ICube, CNRS UMR 7357/Université de Strasbourg, 11 rue Humann, 67085, Strasbourg, France.
| | - Annick Dejaegere
- Biocomputing and Molecular Modelling Laboratory, Integrated Structural Biology Department, Genetics institute of Molecular and Cellular Biology (IGBMC), INSERM U964/CNRS UMR 1704/Strasbourg University, 1 rue Laurent Fries, 67404, Illkirch, France.
| | - Stéphane Viville
- Primordial Germ Cells' Ontogeny and Pluripotency Laboratory, Functional Genomics and Cancer Department, Genetics Institute of Molecular and Cellular Biology (IGBMC), INSERM U964/CNRS UMR 1704/Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France. .,Centre Hospitalier Universitaire, 67000, Strasbourg, France.
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40
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Galliari FC, Carlini AA. Ontogenetic criteria to distinguish vertebral types on the debated xenarthran synsacrum. J Morphol 2014; 276:494-502. [PMID: 25503782 DOI: 10.1002/jmor.20356] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 10/14/2014] [Accepted: 11/18/2014] [Indexed: 11/08/2022]
Abstract
The presence of a synsacrum formed by the fusion of vertebrae that come into closed contact with the ilium and ischium is a feature that characterizes the clade Xenarthra. Nevertheless, the proper identity of each vertebral element that forms it is a matter of discussion. In this article, we provide ontogenetic information about skeletal ossification of the xenarthran synsacrum and define the position of the sacrocaudal limit within it. We analyzed the synsacrum of 25 specimens of nonadult and 101 adult armadillos and anteaters: Dasypus hybridus, D. novemcinctus, Chaetophractus vellerosus, C. villosus, Tamandua tetradactyla, and Myrmecophaga tridactyla. Two sets of vertebrae were identified: an anterior set, often attached to the iliac bones, in which transverse processes are originated mainly from an expansion of the base of the neural arches, and secondarily from a lateroventral ossification center. A posterior set is characterized by a series of vertebrae along which extra lateral ossifications (described here for the first time) are developed and form exclusively the transverse processes. Among armadillos, the sacrocaudal limit is set between the last vertebrae attached to the iliac bones and the first vertebrae that form the dorsal border of the sacroischial fenestra. In addition, anterior free caudals also showed extra lateral ossifications forming exclusively the transverse processes, supporting the notion that more posterior synsacrals are in fact caudal vertebrae that were incorporated to the synsacrum. In pilosans, the sacrocaudal limit is set between the first vertebrae that come into contact with the ischial bones and the immediately anterior one. However, the pattern of homologies is obscured by the low resolution in the ontogenetic sequence when compared to that of armadillos.
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Affiliation(s)
- Fernando C Galliari
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad de Buenos Aires, Buenos Aires, Argentina; División Paleontología de Vertebrados, Museo de La Plata, La Plata, Buenos Aires, Argentina
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41
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Placental Evolution within the Supraordinal Clades of Eutheria with the Perspective of Alternative Animal Models for Human Placentation. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/639274] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Here a survey of placental evolution is conducted. Placentation is a key factor for the evolution of placental mammals that had evolved an astonishing diversity. As a temporary organ that does not allow easy access, it is still not well understood. The lack of data also is a restriction for better understanding of placental development, structure, and function in the human. Animal models are essential, because experimental access to the human placenta is naturally restricted. However, there is not a single ideal model that is entirely similar to humans. It is particularly important to establish other models than the mouse, which is characterised by a short gestation period and poorly developed neonates that may provide insights only for early human pregnancy. In conclusion, current evolutionary studies have contributed essentially to providing a pool of experimental models for recent and future approaches that may also meet the requirements of a long gestation period and advanced developmental status of the newborn in the human. Suitability and limitations of taxa as alternative animal models are discussed. However, further investigations especially in wildlife taxa should be conducted in order to learn more about the full evolutionary plasticity of the placenta system.
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42
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When xenarthrans had enamel: insights on the evolution of their hypsodonty and paleontological support for independent evolution in armadillos. Naturwissenschaften 2014; 101:715-25. [DOI: 10.1007/s00114-014-1208-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 06/26/2014] [Accepted: 07/01/2014] [Indexed: 10/25/2022]
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43
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Ferner K, Siniza S, Zeller U. The Placentation of Eulipotyphla-Reconstructing a Morphotype of the Mammalian Placenta. J Morphol 2014; 275:1122-44. [DOI: 10.1002/jmor.20289] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 04/01/2014] [Accepted: 04/04/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Kirsten Ferner
- Division of Systematic Zoology, Institute of Agriculture and Horticulture; Faculty of Life Science, Humboldt-Universität zu Berlin; Berlin D-10115 Germany
| | - Swetlana Siniza
- Division of Systematic Zoology, Institute of Agriculture and Horticulture; Faculty of Life Science, Humboldt-Universität zu Berlin; Berlin D-10115 Germany
| | - Ulrich Zeller
- Division of Systematic Zoology, Institute of Agriculture and Horticulture; Faculty of Life Science, Humboldt-Universität zu Berlin; Berlin D-10115 Germany
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Karunakaran MM, Göbel TW, Starick L, Walter L, Herrmann T. Vγ9 and Vδ2 T cell antigen receptor genes and butyrophilin 3 (BTN3) emerged with placental mammals and are concomitantly preserved in selected species like alpaca (Vicugna pacos). Immunogenetics 2014; 66:243-54. [PMID: 24526346 DOI: 10.1007/s00251-014-0763-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/27/2014] [Indexed: 11/24/2022]
Abstract
Human Vγ9Vδ2 T cells recognize phosphorylated products of isoprenoid metabolism (phosphoantigens) PAg with TCR comprising Vγ9JP γ-chains and Vδ2 δ-chains dependent on butyrophilin 3 (BTN3) expressed by antigen-presenting cells. They are massively activated in many infections and show anti-tumor activity and so far, they have been considered to exist only in higher primates. We performed a comprehensive analysis of databases and identified the three genes in species of both placental magnorders, but not in rodents. The common occurrence or loss of in silico translatable Vγ9, Vδ2, and BTN3 genes suggested their co-evolution based on a functional relationship. In the peripheral lymphocytes of alpaca (Vicugna pacos), characteristic Vγ9JP rearrangements and in-frame Vδ2 rearrangements were found and could be co-expressed in a TCR-negative mouse T cell hybridoma where they rescued CD3 expression and function. Finally, database sequence analysis of the extracellular domain of alpaca BTN3 revealed complete conservation of proposed PAg binding residues of human BTN3A1. In summary, we show emergence and preservation of Vγ9 and Vδ2 TCR genes with the gene of the putative antigen-presenting molecule BTN3 in placental mammals and lay the ground for analysis of alpaca as candidate for a first non-primate species to possess Vγ9Vδ2 T cells.
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Affiliation(s)
- Mohindar M Karunakaran
- Institute for Virology and Immunobiology, Julius-Maximilian's University of Würzburg, Würzburg, Germany
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45
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Comparative Anatomy of the Petrosal Bone of Dichobunoids, Early Members of Artiodactylamorpha (Mammalia). J MAMM EVOL 2014. [DOI: 10.1007/s10914-014-9254-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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46
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Geiger M, Forasiepi AM, Koyabu D, Sánchez-Villagra MR. Heterochrony and post-natal growth in mammals - an examination of growth plates in limbs. J Evol Biol 2013; 27:98-115. [DOI: 10.1111/jeb.12279] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 10/14/2013] [Indexed: 12/01/2022]
Affiliation(s)
- M. Geiger
- Paläontologisches Institut und Museum der Universität Zürich; Zürich Switzerland
| | | | - D. Koyabu
- University Museum; University of Tokyo; Tokyo Japan
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47
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Rager L, Hautier L, Forasiepi A, Goswami A, Sánchez-Villagra MR. Timing of cranial suture closure in placental mammals: Phylogenetic patterns, intraspecific variation, and comparison with marsupials. J Morphol 2013; 275:125-40. [DOI: 10.1002/jmor.20203] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/05/2013] [Accepted: 08/21/2013] [Indexed: 01/21/2023]
Affiliation(s)
- Lisa Rager
- Paläontologisches Institut und Museum; Universität Zürich, Karl Schmid-Strasse 4; CH-8006 Zürich Switzerland
| | - Lionel Hautier
- Department of Zoology; University of Cambridge; Cambridge CB2 3EJ UK
- Laboratoire de Paléontologie; Institut des Sciences de l'Évolution (ISE-M, UMR-CNRS 5554), C.c. 64, Université Montpellier 2; Place Eugène Bataillon, F-34095 Montpellier Cedex 05 France
| | - Analía Forasiepi
- Paläontologisches Institut und Museum; Universität Zürich, Karl Schmid-Strasse 4; CH-8006 Zürich Switzerland
- CONICET, IANIGLA, CCT-Mendoza; Avda. Ruiz Leal s/n, 5500, Mendoza Mendoza Argentina
| | - Anjali Goswami
- Department of Genetics; Evolution and Environment, University College London; London UK
| | - Marcelo R. Sánchez-Villagra
- Paläontologisches Institut und Museum; Universität Zürich, Karl Schmid-Strasse 4; CH-8006 Zürich Switzerland
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Layer 4 in primary visual cortex of the awake rabbit: contrasting properties of simple cells and putative feedforward inhibitory interneurons. J Neurosci 2013; 33:11372-89. [PMID: 23843510 DOI: 10.1523/jneurosci.0863-13.2013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Extracellular recordings were obtained from two cell classes in layer 4 of the awake rabbit primary visual cortex (V1): putative inhibitory interneurons [suspected inhibitory interneurons (SINs)] and putative excitatory cells with simple receptive fields. SINs were identified solely by their characteristic response to electrical stimulation of the lateral geniculate nucleus (LGN, 3+ spikes at >600 Hz), and simple cells were identified solely by receptive field structure, requiring spatially separate ON and/or OFF subfields. Notably, no cells met both criteria, and we studied 62 simple cells and 33 SINs. Fourteen cells met neither criterion. These layer 4 populations were markedly distinct. Thus, SINs were far less linear (F1/F0 < 1), more broadly tuned to stimulus orientation, direction, spatial and temporal frequency, more sensitive to contrast, had much higher spontaneous and stimulus-driven activity, and always had spatially overlapping ON/OFF receptive subfields. SINs responded to drifting gratings with increased firing rates (F0) for all orientations and directions. However, some SINs showed a weaker modulated (F1) response sharply tuned to orientation and/or direction. SINs responded at shorter latencies than simple cells to stationary stimuli, and the responses of both populations could be sustained or transient. Transient simple cells were more sensitive to contrast than sustained simple cells and their visual responses were more frequently suppressed by high contrasts. Finally, cross-correlation between LGN and SIN spike trains confirmed a fast and precisely timed monosynaptic connectivity, supporting the notion that SINs are well suited to provide a fast feedforward inhibition onto targeted cortical populations.
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Maseko BC, Patzke N, Fuxe K, Manger PR. Architectural Organization of the African Elephant Diencephalon and Brainstem. BRAIN, BEHAVIOR AND EVOLUTION 2013; 82:83-128. [DOI: 10.1159/000352004] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/03/2013] [Indexed: 11/19/2022]
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50
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Straehl FR, Scheyer TM, Forasiepi AM, MacPhee RD, Sánchez-Villagra MR. Evolutionary patterns of bone histology and bone compactness in xenarthran mammal long bones. PLoS One 2013; 8:e69275. [PMID: 23874932 PMCID: PMC3706384 DOI: 10.1371/journal.pone.0069275] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 06/06/2013] [Indexed: 11/19/2022] Open
Abstract
Bone microstructure reflects physiological characteristics and has been shown to contain phylogenetic and ecological signals. Although mammalian long bone histology is receiving increasing attention, systematic examination of the main clades has not yet been performed. Here we describe the long bone microstructure of Xenarthra based on thin sections representing twenty-two species. Additionally, patterns in bone compactness of humeri and femora are investigated. The primary bone tissue of xenarthran long bones is composed of a mixture of woven, parallel-fibered and lamellar bone. The vascular canals have a longitudinal, reticular or radial orientation and are mostly arranged in an irregular manner. Concentric rows of vascular canals and laminar organization of the tissue are only found in anteater bones. The long bones of adult specimens are marked by dense Haversian bone, a feature that has been noted for most groups of mammals. In the long bones of armadillos, secondary osteons have an oblique orientation within the three-dimensional bone tissue, thus resulting in their irregular shape when the bones are sectioned transversely. Secondary remodeling is generally more extensive in large taxa than in small taxa, and this could be caused by increased loading. Lines of arrested growth are assumed to be present in all specimens, but they are restricted to the outermost layer in bones of armadillos and are often masked by secondary remodeling in large taxa. Parameters of bone compactness show a pattern in the femur that separates Cingulata and Pilosa (Folivora and Vermilingua), with cingulates having a lower compactness than pilosans. In addition, cingulates show an allometric relationship between humeral and femoral bone compactness.
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Affiliation(s)
- Fiona R. Straehl
- Paläontologisches Institut und Museum, Universität Zürich, Zürich, Switzerland
| | - Torsten M. Scheyer
- Paläontologisches Institut und Museum, Universität Zürich, Zürich, Switzerland
| | | | - Ross D. MacPhee
- Vertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
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